User: muraved

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muraved0
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Posts by muraved

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Comment: C: How exactly does MAQ handle mate-pair data
... Oops... thanks for pointing that out, I must've missed that :-/ ...
written 12 months ago by muraved0
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Answer: A: How exactly does MAQ handle mate-pair data
... Thanks. Hmm, so, there is no input specification of whether it's paired-end or mate-pair. For an input like maq map F.fq R.fq, it simpy checks the relative positions of mapping locations, and accepts F-R as specified by -a, and R-F as specified by -A then? ...
written 12 months ago by muraved0
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Comment: C: How exactly does MAQ handle mate-pair data
... As you will notice, my question has the exact same link you provided. The specifics I am asking for are not explained on the man page in my opinion. But maybe I'm overlooking something. ...
written 12 months ago by muraved0
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Comment: C: How exactly does MAQ handle mate-pair data
... Thanks for the link. I am well aware of several read mappers for MP mapping, I'm really asking specifically about MAQ. I do appreciate your help, though :-) ...
written 12 months ago by muraved0
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Comment: C: How exactly does MAQ handle mate-pair data
... Yes. The way it does consensus calling lends itself to read correction. I'm not so much interested in the alignment itself. Also, old doesn't mean bad ;-) ...
written 12 months ago by muraved0
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How exactly does MAQ handle mate-pair data
... Hi, I'm trying to align a 3.5K-insert mate-pair library using MAQ 0.7.0. From the man page ([http://maq.sourceforge.net/maq-manpage.shtml][1]), it is not quite clear to me how exactly MAQ handles the outward orientation of such reads, and how it distinguished paired-end input from mate-pair input. ...
alignment sequence mate-pair maq written 12 months ago by muraved0
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Comment: C: samtools depth for start positions
... > This is true only if the read mapped to forward strand. Good point! My goal is to make coverage statistically independent between adjacent positions (which they are not for pileup data, since mapping a read to position x adds counts to its neighbors). In case of the reverse strand, I need what ...
written 21 months ago by muraved0
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Comment: C: samtools depth for start positions
... Yes. Using ediff1d, pileup contains the number of changes in coverage. It is equivalent to the number of reads starting there minus the number of reads ending at i-1, i.e. it undercounts the number of start reads by the ones ending right before. In the loop, pileup[i] contains the number of starting ...
written 21 months ago by muraved0
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samtools depth for start positions
... Hi, I am trying to obtain the number of reads starting at each position from a bam file. I've used samtools depth -aa ${bamfile} | cut -f 3 > ${pileupFile} to create a depth of coverage per position, and confirmed that all reads have length 100 using samtools view ${bamfile} | awk ...
samtools depth of coverage written 21 months ago by muraved0 • updated 21 months ago by geek_y8.6k
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Allele intensities from SNP arrays
... Hi everyone, I am attempting to extract what I think should be the most basic information on SNP arrays from CEL files: intensity values for alleles A and B, and their respective genomic position, but no genotype calls or anything like that. I have attempted that using packages in Bioconductor (lik ...
R snp cnv written 4.1 years ago by muraved0

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